Diagram of how a job gets run on Lonestar
Explanation
Start at the bottom - that's what you want: one of Lonestar's 1,888 compute nodes running your specific program (bowtie mapping in this case).
To get there, you must go through a "Queue Manager" program running on a different computer - the login (or "head") node. This program keeps track of what's running on those 1,888 nodes and what's in line to run next. It's very good at doing this.
You tell the Queue Manager what you want done via "job.sge" - your job submission script. That specifies how many nodes you need, what allocation to use, the maximum run time of the job, etc. The Queue Manager doesn't really care what you're running, just how you want it run. It needs to pass info on what you're running off to the compute node - you do that with the line setenv CONTROL_FILE commands.
The Queue Manager sends off the commands in the file commands to the compute nodes; so commands is really the first thing to start with.
The launcher_creator.py script just helps you by creating jobs.sge easily - saves you some time editing a file (and potentially messing it up).